Morphological pseudotime ordering and fate mapping reveal diversification of cerebellar inhibitory interneurons

Understanding how diverse neurons are assembled into circuits requires a framework for describing cell types and their developmental trajectories. Here we combine genetic fate-mapping, pseudotemporal profiling of morphogenesis, and dual morphology and RNA labeling to resolve the diversification of mouse cerebellar inhibitory interneurons. Molecular layer interneurons (MLIs) derive from a common progenitor population but comprise diverse dendritic-, somatic-, and axon initial segment-targeting interneurons. Using quantitative morphology from 79 mature MLIs, we identify two discrete morphological types and presence of extensive within-class heterogeneity. Pseudotime trajectory inference using 732 developmental morphologies indicate the emergence of distinct MLI types during migration, before reaching their final positions. By comparing MLI identities from morphological and transcriptomic signatures, we demonstrate the dissociation between these modalities and that subtype divergence can be resolved from axonal morphogenesis prior to marker gene expression. Our study illustrates the utility of applying single-cell methods to quantify morphology for defining neuronal diversification. Morphology and spatial context are often dissociated from single-cell studies of neuronal diversity. Here the authors trace cerebellar interneurons through lineage, morphology and transcriptomics, and show that diversification can be resolved during morphogenesis.

Automated summary

Understanding the diversification of neuronal circuits in the cerebellum is crucial, and this study provides novel insights by combining genetic fate-mapping, morphological profiling, and molecular labeling techniques. The authors identify diverse types of molecular layer interneurons (MLIs) that arise from a common progenitor population. They demonstrate that MLIs can be categorized into two distinct morphological types with extensive within-class heterogeneity. Moreover, they show that subtype divergence can be resolved based on axonal morphogenesis before marker gene expression. This study highlights the importance of single-cell methods in quantifying neuronal diversification and sheds light on the dissociation between morphology and transcriptomics in understanding neuronal diversity.